MicrobiomeR
MicrobiomeR: An R Package for Simplified and Standardized Microbiome Analysis Workflows - Published in JOSS (2019)
pycirclize
Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)
cogclassifier
A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category
pybarrnap
Python implementation of barrnap (Bacterial ribosomal RNA predictor)
phylotoast
Tools for phylogenetic data analysis including visualization and cluster-computing support.
aniclustermap
A tool for drawing ANI clustermap between all-vs-all microbial genomes
pagoo
A comprehensive and intuitive encapsulated OO class system for analyzing bacterial pangenomes in R.
https://github.com/cidgoh/nf-ncov-voc
A Nextflow wrapped workflow for generating the mutation profiles of SARS-CoV-2 or Mpox genomes. Workflow is developed in collaboration with VIRUS-MVP (https://github.com/cidgoh/VIRUS-MVP) which can be used to visualize the mutation profiles and functional annotations.
submitdatairidanext
Pipeline for submitting data to INSDC databases for IRIDA Next
bacpaq
Bacterial Genomics workflow for short(Illumina) and long-read (Oxford Nanopore) sequencing data
metasbt
A scalable framework for automatically indexing microbial genomes and accurately characterizing metagenome-assembled genomes with Sequence Bloom Trees